Andreas M��ller [Fri, 22 May 2015 12:24:34 +0000 (12:24 +0000)]
merge trunk into model change 3.6
Andreas M��ller [Fri, 22 May 2015 11:53:01 +0000 (11:53 +0000)]
adapt nonViralNameParser to model changes
Andreas M��ller [Fri, 22 May 2015 11:51:38 +0000 (11:51 +0000)]
updated NonViralNameParserImplTest
Andreas M��ller [Fri, 22 May 2015 11:50:29 +0000 (11:50 +0000)]
update schemaUpdater35_36
Andreas M��ller [Fri, 22 May 2015 11:49:52 +0000 (11:49 +0000)]
add MnTableRemover
Andreas M��ller [Fri, 22 May 2015 11:49:35 +0000 (11:49 +0000)]
cleanup
Andreas M��ller [Fri, 22 May 2015 11:49:06 +0000 (11:49 +0000)]
cleanup
Andreas M��ller [Fri, 22 May 2015 11:48:29 +0000 (11:48 +0000)]
adapt ModelUpdate tester
Andreas M��ller [Thu, 21 May 2015 14:36:16 +0000 (14:36 +0000)]
integrate parameters into constructor for updaters
Cherian Mathew [Thu, 21 May 2015 14:23:41 +0000 (16:23 +0200)]
added dirs and files to ignore
Andreas M��ller [Wed, 20 May 2015 15:39:11 +0000 (15:39 +0000)]
added id to uuidAndTitleCache #4799 (bugfix)
Andreas M��ller [Wed, 20 May 2015 15:23:31 +0000 (15:23 +0000)]
added id to uuidAndTitleCache
Andreas Kohlbecker [Wed, 20 May 2015 14:38:56 +0000 (16:38 +0200)]
increasing the permGenSpace in the eclipse launcher
Andreas Kohlbecker [Wed, 20 May 2015 14:38:26 +0000 (16:38 +0200)]
fixing problem with missing autinitialization of titleCaches, contributes to #4919
Patric Plitzner [Wed, 20 May 2015 12:03:56 +0000 (12:03 +0000)]
- implemented importing of DNA ABCD units
- DNA sampled will be attached to already existing specimens
- re-enabled tests
Andreas Kohlbecker [Wed, 20 May 2015 11:05:38 +0000 (13:05 +0200)]
sloving NPE in AdvancedBeanInitializer
Andreas Kohlbecker [Wed, 20 May 2015 09:27:27 +0000 (11:27 +0200)]
fixing bug related to generic types
Andreas Kohlbecker [Tue, 19 May 2015 14:54:28 +0000 (16:54 +0200)]
further performance improvements: - better autoinitialization of collection items, - fixing bug in AdvancedBeanInitializer: adding missing LEFT to JOIN FETCH
Andreas Kohlbecker [Tue, 19 May 2015 12:33:55 +0000 (14:33 +0200)]
fixing bug in matchesLevel method
Andreas Kohlbecker [Tue, 19 May 2015 12:31:46 +0000 (14:31 +0200)]
adding missing sources
Cherian Mathew [Tue, 19 May 2015 10:05:59 +0000 (10:05 +0000)]
removed vaadin dependency
Patric Plitzner [Mon, 18 May 2015 15:10:39 +0000 (15:10 +0000)]
- added tests to ignore because other tests fail :-/
Andreas Kohlbecker [Mon, 18 May 2015 14:40:43 +0000 (16:40 +0200)]
speed up of DistributionTree.orderAsTree() by factor 1.6
Andreas Kohlbecker [Mon, 18 May 2015 14:36:09 +0000 (16:36 +0200)]
setting source dependencies for m2e enviromnent
Andreas Kohlbecker [Mon, 18 May 2015 14:35:14 +0000 (16:35 +0200)]
adding method to get the intentifier from hibernate proxies
Andreas Kohlbecker [Mon, 18 May 2015 09:01:25 +0000 (11:01 +0200)]
increasing the permGenSpace for profiling sessions
Andreas Kohlbecker [Mon, 18 May 2015 09:00:47 +0000 (11:00 +0200)]
performance improvement by 42% by using default initstrategy for composeDistributionInfoFor()
Patric Plitzner [Mon, 18 May 2015 14:40:04 +0000 (14:40 +0000)]
- re-enabled and fixed ABCD import tests(#4910)
Patric Plitzner [Mon, 18 May 2015 14:35:43 +0000 (14:35 +0000)]
- added null check
Patric Plitzner [Mon, 18 May 2015 14:09:48 +0000 (14:09 +0000)]
- improved name matching for NamedAreas (continents) in ABCD import (#4910)
- added null check
- fixed ggbn extension check
Patric Plitzner [Mon, 18 May 2015 06:51:53 +0000 (06:51 +0000)]
- optimized name matching for terms in ABCD import
Andreas M��ller [Thu, 14 May 2015 07:23:32 +0000 (07:23 +0000)]
try to fix ConcurrentModificationException in ValidationExcecutorTest #4851
Andreas Kohlbecker [Wed, 13 May 2015 09:08:52 +0000 (11:08 +0200)]
fixing further bean field property mapping probelm, contributes to #3841: resolve bean inconsistencies
Andreas Kohlbecker [Tue, 12 May 2015 19:15:29 +0000 (21:15 +0200)]
adding missing @Transient
Patric Plitzner [Wed, 13 May 2015 08:56:06 +0000 (08:56 +0000)]
- made service methods public
- added java doc
- fixed typo
Patric Plitzner [Wed, 13 May 2015 08:06:25 +0000 (08:06 +0000)]
- added option to retrieve indirectly associated specimen
- added service method to retrieve the completete derivative hierarchy for a given specimen
- added test
Andreas Kohlbecker [Tue, 12 May 2015 15:18:45 +0000 (17:18 +0200)]
fixing #4179 (improve performance of portal/taxon/{uuid}/media)
Andreas Kohlbecker [Tue, 12 May 2015 15:01:06 +0000 (17:01 +0200)]
adding log4j.properties in user home to launcher
Andreas Kohlbecker [Tue, 12 May 2015 09:58:36 +0000 (11:58 +0200)]
fixing #4903 (SQLGrammarException exception in description/namedAreasInUse)
Andreas Kohlbecker [Tue, 12 May 2015 09:07:53 +0000 (11:07 +0200)]
adding forceSchemaUpdate to the cdmlib-remote-webapp launcher
Patric Plitzner [Tue, 12 May 2015 08:47:55 +0000 (08:47 +0000)]
- added config option to ignore already existing specimens during import
- for ggbn import already existing specimens are searched and attached if associated to the dna unit
- refactored AbcdReport to also display the unitId
Patric Plitzner [Tue, 12 May 2015 08:44:05 +0000 (08:44 +0000)]
- added significantIdentifer as search parameter to occurrenceService.findByTitle()
Patric Plitzner [Mon, 11 May 2015 12:03:43 +0000 (12:03 +0000)]
- added modifying text to factual data label #4883
Katja Luther [Mon, 11 May 2015 11:37:29 +0000 (11:37 +0000)]
make the taxonomic tree editable in natural order (see #3771), adding comparator
Katja Luther [Mon, 11 May 2015 10:16:00 +0000 (10:16 +0000)]
delete the embedded class UuidAndTitleCacheOfAcceptedTaxon
Andreas M��ller [Mon, 11 May 2015 10:06:11 +0000 (10:06 +0000)]
privates for uuidAndTitleCache
Patric Plitzner [Wed, 6 May 2015 16:26:48 +0000 (16:26 +0000)]
- added count to single reads in portal
Andreas M��ller [Wed, 6 May 2015 15:46:15 +0000 (15:46 +0000)]
add update script and JAXB annotation for sequence positions #4743
Andreas M��ller [Wed, 6 May 2015 15:38:32 +0000 (15:38 +0000)]
Adding firstSeqPosition, leftCutPosition and rightCutPosition to SingleReadAlignment #4743 , Update script still missing
Patric Plitzner [Wed, 6 May 2015 12:49:41 +0000 (12:49 +0000)]
- changed "derivate" to "derivatives"
Andreas M��ller [Tue, 5 May 2015 15:52:52 +0000 (15:52 +0000)]
update script for removing unique key on supportedCategoricalEnums and recommendedModifierEnums #4843
Andreas M��ller [Tue, 5 May 2015 14:51:04 +0000 (14:51 +0000)]
change SupportedCategoricalEnumeration and RecommendedModifierEnumeration from OneToMany to ManyToMany #4843
Andreas M��ller [Tue, 5 May 2015 12:50:32 +0000 (12:50 +0000)]
implement datasource type inference for external datasources: #3910
Patric Plitzner [Tue, 5 May 2015 11:36:12 +0000 (11:36 +0000)]
- show primer information in specimen tab although no contig file specified
Cherian Mathew [Mon, 4 May 2015 14:58:01 +0000 (14:58 +0000)]
updated cdm-vaadin version to 3.5.2-SNAPSHOT
edit-jenkins [Mon, 4 May 2015 11:56:06 +0000 (11:56 +0000)]
[maven-release-plugin] prepare for next development iteration
edit-jenkins [Mon, 4 May 2015 11:56:01 +0000 (11:56 +0000)]
[maven-release-plugin] prepare release cdmlib-parent-3.5.1
Katja Luther [Mon, 4 May 2015 10:06:53 +0000 (10:06 +0000)]
Katja Luther [Mon, 4 May 2015 10:00:04 +0000 (10:00 +0000)]
Katja Luther [Mon, 4 May 2015 09:57:29 +0000 (09:57 +0000)]
Katja Luther [Mon, 4 May 2015 09:12:59 +0000 (09:12 +0000)]
Katja Luther [Mon, 4 May 2015 09:02:13 +0000 (09:02 +0000)]
Katja Luther [Mon, 4 May 2015 07:47:33 +0000 (07:47 +0000)]
Andreas M��ller [Thu, 30 Apr 2015 22:14:18 +0000 (22:14 +0000)]
minor
Andreas M��ller [Thu, 30 Apr 2015 22:12:59 +0000 (22:12 +0000)]
Implement bidirectionality for QuantitativeData-StatisticalMeasurementValue #4845
Andreas M��ller [Thu, 30 Apr 2015 22:10:09 +0000 (22:10 +0000)]
fix stateData removal #4840
Andreas M��ller [Thu, 30 Apr 2015 19:23:28 +0000 (19:23 +0000)]
add validation rule request for idInVocabulary #3379, #4245
Andreas M��ller [Thu, 30 Apr 2015 19:17:49 +0000 (19:17 +0000)]
minor
Alexander Oppermann [Thu, 30 Apr 2015 12:48:41 +0000 (12:48 +0000)]
Partial Fix of Ticket #4728
Andreas Kohlbecker [Thu, 30 Apr 2015 10:08:31 +0000 (12:08 +0200)]
solving problem in #4803 (Upgrade dbunit and easymock)
Andreas Kohlbecker [Thu, 30 Apr 2015 10:03:09 +0000 (12:03 +0200)]
ignore
Andreas Müller [Wed, 29 Apr 2015 15:37:46 +0000 (15:37 +0000)]
fix remove hybrid method (related to #2576)
Andreas Müller [Wed, 29 Apr 2015 15:26:28 +0000 (15:26 +0000)]
added not blank handling for potential notEmpty strings #4653
Andreas Müller [Wed, 29 Apr 2015 15:24:26 +0000 (15:24 +0000)]
added not blank handling for potential notEmpty strings #4653 , solving compilation issues
Alexander Oppermann [Wed, 29 Apr 2015 15:22:30 +0000 (15:22 +0000)]
Partial fix of Ticket #4728
Andreas Müller [Wed, 29 Apr 2015 15:18:12 +0000 (15:18 +0000)]
added not blank handling for potential notEmpty strings #4653
Andreas Müller [Wed, 29 Apr 2015 11:43:37 +0000 (11:43 +0000)]
minor
Andreas Müller [Wed, 29 Apr 2015 11:41:21 +0000 (11:41 +0000)]
fix move description element bug #4806
Andreas Müller [Wed, 29 Apr 2015 09:49:41 +0000 (09:49 +0000)]
minor
Andreas Müller [Mon, 27 Apr 2015 16:00:09 +0000 (16:00 +0000)]
fix XmlType.propOrder #4840
Andreas Müller [Mon, 27 Apr 2015 15:47:27 +0000 (15:47 +0000)]
implement bidirectionality on CategoricalData-StateData #4840
Andreas Müller [Mon, 27 Apr 2015 14:53:08 +0000 (14:53 +0000)]
fix relationship type for CategoricalData-StateData #3382
Cherian Mathew [Mon, 27 Apr 2015 14:22:56 +0000 (14:22 +0000)]
updating vaadin version
Andreas Müller [Fri, 24 Apr 2015 09:46:54 +0000 (09:46 +0000)]
Changed order of PresenceAbsence terms according to E+M ordering #3906
Andreas Müller [Fri, 24 Apr 2015 08:37:18 +0000 (08:37 +0000)]
Remove left join from listNamedAreasInUse #4820
Patric Plitzner [Fri, 24 Apr 2015 07:06:47 +0000 (07:06 +0000)]
- order character data by key name
Andreas Müller [Wed, 22 Apr 2015 13:40:17 +0000 (13:40 +0000)]
Capital letters for term types, related to #4553
Katja Luther [Wed, 22 Apr 2015 11:50:15 +0000 (11:50 +0000)]
Katja Luther [Wed, 22 Apr 2015 11:36:27 +0000 (11:36 +0000)]
Andreas Müller [Wed, 22 Apr 2015 08:51:49 +0000 (08:51 +0000)]
fix hybrid parsing with existing hybrid relationships on full reference parsing #2576
Andreas Müller [Tue, 21 Apr 2015 21:50:18 +0000 (21:50 +0000)]
fix parsing of hybrids as fullReferenceName #2576
Andreas Müller [Tue, 21 Apr 2015 18:00:29 +0000 (18:00 +0000)]
minor
Andreas Müller [Tue, 21 Apr 2015 17:54:18 +0000 (17:54 +0000)]
fix hybrid parsing with existing hybrid relationships #2576
Andreas Kohlbecker [Tue, 21 Apr 2015 14:41:41 +0000 (14:41 +0000)]
fixing #4752 (RL Webservice 9: CommonName Webservice)
Andreas Müller [Tue, 21 Apr 2015 14:34:48 +0000 (14:34 +0000)]
fixing infinite loop in HybridRelationship.compareTo #2576
Andreas Müller [Tue, 21 Apr 2015 14:27:57 +0000 (14:27 +0000)]
cleanup NonViralNameServer doc
Andreas Müller [Tue, 21 Apr 2015 14:26:31 +0000 (14:26 +0000)]
fix isSection #4556
Patric Plitzner [Tue, 21 Apr 2015 12:46:44 +0000 (12:46 +0000)]
- reverted sorting order of field units
Andreas Müller [Tue, 21 Apr 2015 12:20:09 +0000 (12:20 +0000)]
Add millimeter (mm) as new measurement unit
Patric Plitzner [Tue, 21 Apr 2015 05:14:35 +0000 (05:14 +0000)]
- split up DTO images in specimen scans and detail images